Here's my 2 cents from working in a vet clinic:
Employed staff do not earn alot of money. Which means, unless your vet is THE boss, he or she is getting a flat rate pay per month, whether he/she does overtime. The cost of vaccinations, blood tests, surgeries etc are usually set by the boss already, and they just have to charge it out. Vets will have studied for 5-6 years but their salary is frankly very low compared to other professions out there.
There are a lot of hidden costs that you don't see. Syringes, needles, gauze, swabs, disinfecting and cleaning agents, blood vacutainers, machine upkeep, xray films, xray chemicals, etc etc. If you have a boisterous dog that doesn't keep still when doing blood tests, then we may have to use for eg 3 syringes and 3 needles to successfully draw blood, because we don't keep jabbing with the same needle (goes blunt). And also nurses. You're paying for their time, their care and their physical handling of your pet. Plus feeding, watering, walking, cleaning out cages etc.
If your pet is difficult to handle, sedation is required. They may be loving, placid and good-natured with you, their owner, but when they're feeling ill, plus thrust into a new scary environment with strangers who are trying to stick needles into them, they get scared, and some animals get aggressive and therefore dangerous to their handlers. No vet staff wants to be scratched, bitten or mauled by a scared animal, hence the sedation.
It is scientifically proven that if you neuter a female dog before her first heat, there is like an 80% risk reduction in developing reproductive cancer down the road. Also it prevents against getting pyometra which is a uterine infection with pus and can be fatal if not rushed into emergency surgery.. by then you'd be paying $1000 easy for that procedure along with fluids, tests, recovery care. Same goes for male dogs, neutering them early helps prevent aggression related problems and reproductive problems.
Having said all that, there are some clinics that do charge more for the same services. Sometimes they can get away with that if they are the sole clinic on a mountain, for e.g. Or, if they are a 24 hour hospital facility, because they have specialists working there. What you truly should be paying for is the level of client care and communication. There is no point going to the cheapest vet around if he/she will not treat your pet with respect.